From: Sebastian Stolzenberg (s.stolzenberg_at_gmail.com)
Date: Sun Nov 08 2009 - 19:24:12 CST
>> I assume now that the SHAKE algorithm imposes restraints on all the IC
>> coordinates involving the particular hydrogen to be constrained.
> that is not correct. you constrain what you define to constrain. typically,
> the water molecules completely and all other bonds involving hydrogens.
>> Then, what if I have a hydrogen attached to a backbone nitrogen? What about
>> hydrogens attached to carbons along the side chains?
> very simple: each "shaken" bond or angle is equivalent to removing one
> DOF. so waters have 6 DOFs instead of 9. if you go to more complex
> constraints it can become very complicated.
Thank you, so I can calculate n_DOF for the water molecules now because
I know that two bonds and one angle are constrained for each water molecule.
However, for (non-water) heavy atom hydrogens, I cannot tell whether the
NAMD command "rigidBonds all" only constrains bonds, or also (which)
angles, etc., as is done for the waters.
I took a look at the NAMD source code, but "grep"ing the whole source
code folder for
did not yield anything about additional angle, dihedral,... constraints.
Also, the most current paper (2009) on CHARMM refers to SHAKE only in
terms of "fixing the relative positions of..."
Can I thus assume that "rigidBonds all" really only constrains bonds
(for hydrogens attached to non-water heavy atoms)? If no, what angles
does NAMD "rigidBonds all" constrain for the protein?
Thank you very much for your help,
>> I am worried to have to deal with dihedral constraints to determine
>> n_DOF..... although the original SHAKE paper by RYCKAERT JCP 1977 does not
>> mention dihedrals...
> i don't think an over 30 year old paper is a good reference for modern
> techniques. the same goes for the NAMD tutorial. the former is just the original
> idea (nobody reads the original ewald sum paper to learn how to implement ewald
> sum in a modern MD code), the latter is a means to get you started _without_
> presenting too many confusing details.
> why don't you have a look at some of the (many) more recent books
> on MD simulation techniques and papers about the implementation of
> current package MD codes (there is at least one for every major MD package
> and i would recommend to not discard those about packages you don't use).
> p.s.: since you are curious about methods, you should take note that SHAKE
> is only half the story and that you have your constrained bonds
> RATTLEd as well. ;)
>> Thanks a bunch,
>> Sebastian Stolzenberg wrote:
>>> Hi Axel,
>>>> very simple: each "shaken" bond or angle is equivalent to removing one
>>>> DOF. so waters have 6 DOFs instead of 9. if you go to more complex
>>>> constraints it can become very complicated.
>>> SHAKE *angles*?? The NAMD tutorial doesn't mention anything about them.
>>> Or was your reasoning now more in general for educational purposes?
>>> Would you have some DOF reading recommendations at hand for the more
>>> complicated (e.g. dihedral) constraints cases? (just for my own curiosity
>>> and to maintain my astonishment :o) )
>>> Thanks a lot,
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